Motivated by ecological communities to develop tools for multi-dimensional time series
Collage of rodent species from the Portal Project; https://portal.naturecast.org/profiles.html
Motivated by ecological communities to develop tools for multi-dimensional time series
Collage of rodent species from the Portal Project; https://portal.naturecast.org/profiles.html
Motivated by ecological communities to develop tools for multi-dimensional time series
Time series of rodent populations
Motivated by ecological communities to develop tools for multi-dimensional time series
Time series of rodent populations with putative qualitative changes noted
Quantify how ecosystems are responding to stressors
Phase plane of precipitation and temperature at Portal over time
Need to distinguish
Time series of rodent populations zoomed in to moons 200 to 400
Title of Christensen et al 2018 Ecology Report
Christensen et al. 2018 established methods
Screencap of LDATS on CRAN; https://cran.r-project.org/web/packages/LDATS/index.html
Two-stage analyses:
Latent Dirichlet Allocation
\(M\) total documents
\(N\) total words
\(w\) word identity
\(z\) topic identity
\(\theta\) topics-in-documents
\(\alpha\) Dirichlet parameter for \(\theta\)
\(\beta\) terms-in-topics
Plate notation for Latent Dirichlet Allocation
Bookshelf
Latent Dirichlet Allocation
Matrix decomposition representation of LDA
Bookshelf
Latent Dirichlet Allocation
Matrix decomposition representation of LDA with ecological terms
Collage of rodent species from the Portal Project; https://portal.naturecast.org/profiles.html
Latent Dirichlet Allocation
Matrix decomposition representation of LDA with ecological terms and Gamma bolded
Collage of rodent species from the Portal Project; https://portal.naturecast.org/profiles.html
Abrupt change points
Fit using parallel tempering MCMC
LDATS PackageTop-level API target: an “lm-style”
LDA_TS(data, topics = 2, nseeds = 1, formulas = ~1, nchangepoints = 0, timename = "time", weights = TRUE, control = list())
LDATS PackageUnder-the-hood
LDATS PackageReleased on CRAN
LDATS PackageIn development on GitHub
A caption
National Science Foundation: DEB-1622425, DGE-1315138, DGE-1842473
Gordon and Betty Moore Foundation: Data-Driven Discovery Initiative Grant GBMF4563